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AWGL / somatic_db

A database for analysing cancer NGS data within AWMGS
https://awgl.github.io/somatic_db/
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Manual variant validation #108

Closed Istaisa closed 6 months ago

Istaisa commented 6 months ago

Edited the manual variant format check so that variants just outside the ROI can be added. Have currently set cutoff (max_acceptable_distance) at 20bp but feel free to change. Unit tests updated. Fixes #106

SophieS9 commented 6 months ago

Error when using the form outside of bed region (and on the boundary): Internal Server Error: /analysis/326 Traceback (most recent call last): File "/home/sophieshaw/miniconda3/envs/somatic_variant_db/lib/python3.8/site-packages/django/core/handlers/exception.py", line 34, in inner response = get_response(request) File "/home/sophieshaw/miniconda3/envs/somatic_variant_db/lib/python3.8/site-packages/django/core/handlers/base.py", line 115, in _get_response response = self.process_exception_by_middleware(e, request) File "/home/sophieshaw/miniconda3/envs/somatic_variant_db/lib/python3.8/site-packages/django/core/handlers/base.py", line 113, in _get_response response = wrapped_callback(request, *callback_args, *callback_kwargs) File "/home/sophieshaw/miniconda3/envs/somatic_variant_db/lib/python3.8/site-packages/django/contrib/auth/decorators.py", line 21, in _wrapped_view return view_func(request, args, **kwargs) File "/home/sophieshaw/somatic_db/analysis/views.py", line 575, in analysis_sheet variant_check, warning_message = variant_format_check(new_variant_data['chrm'], new_variant_data['position'], new_variant_data['ref'], new_variant_data['alt'], sample_obj.panel.bed_file.path, new_variant_data['total_reads'], new_variant_data['alt_reads']) File "/home/sophieshaw/somatic_db/analysis/utils.py", line 1075, in variant_format_check closest_match = min(variant_bed_region.absolute_distance(panel_bed)) ValueError: min() arg is an empty sequence